Chapter 5

A New Science: Biome Care

The final chapter expands the concept into a new field of study: Biome Care. Rather than focusing exclusively on pharmaceuticals or probiotics, this discipline emphasizes habitat design inside the body.
By restoring cellulose-rich environments, physicians and researchers may transform approaches to inflammation, digestion, and microbial therapy. The chapter calls for a new generation of researchers willing to reconsider the foundations of human physiology.


Suggested Subtitles
• From Medicine to Habitat Engineering
• Why Microbiome Science Is Stuck
• The Limits of Probiotics and Fecal Transplants
• Designing the Intestinal Ecosystem
• The Future of Human Health


Protocol for Human Biome
Feeding and Waste Elimination
1. Purpose

This chapter presents a structured protocol for feeding and maintaining the human intestinal biome while supporting orderly elimination of metabolic waste.
The approach prioritizes the ecological needs of the intestinal environment—particularly the large intestine—by ensuring continuous structural bulk (cellulose), controlled fermentation substrates, and staged nutritional refeeding.

The central premise is that the intestinal biome functions optimally when the intestine maintains physical volume and pressure, comparable to a properly inflated bicycle tire: not empty, but filled with structured plant material that supports microbial activity and waste transport.

2. Core Biological Assumptions

2.1 Five-Day Food Cycle
The protocol assumes a five-day digestive cycle:
Physiological Phase
Day 1–3
Intestine conditoning prior to food processing and biochemical extraction
Day 3–5
Fermentation and Waste managing and elimination.
Elimination proceeds in stages:
Complex material removal first - dense or chemically complex residues are expelled first, together with lymphatic and systemic metabolic wastes. Macronutrient residues and remaining fats, proteins, and carbohydrate remnants are eliminated.

Cellulose exit phase
Structural plant matter leaves the intestine last, acting as the physical scrubber and support of the microbioms of the stomach that handle left over prior waste material.
This staged process allows the intestine to function as a biological reactor system.

3. Guiding Principles
Biome First - the protocol prioritizes the intestinal ecosystem rather than caloric intake.

Structural Bulk
Cellulose acts as:
• physical scaffolding
• microbial habitat
• fermentation substrate
• waste scrubbing medium

Controlled Fermentation
Sugars and simple plant foods feed microbial fermentation once cellulose is established.

Sequential Nutrition
Nutrient density is introduced progressively, allowing microbial populations and host metabolism to adapt.

4. Protocol Phases
Phase 1 — Initiation Fast
Duration: up to 5 days (initial protocol uses 1 day)
Purpose:
• trigger elimination (Solid, liquid and gas)
• clear intestinal residues
• reset feeding sequence

Characteristics:
Strong elimination of liquids and matter often occurs on the first day of fasting.

After this phase, elimination may temporarily decrease.

For first-time participants, a one-day fast is sufficient to begin the protocol.

Phase 2 — Structural Refill (Cellulose Phase)
The second day begins the intestinal refill process.
Primary goal:
Re-establish intestinal volume using non-digestible plant material.
Like materials:
• The stems of Spinach, Basil, Cilantro, Bamboo and alfalfa shoots fresh and sun dried.
• uncooked leaves fresh and sun dried
• fibrous vegetables, fresh and sun dried
• Grated uncooked tubers, fresh and sun dried.
• mushrooms
• other low-absorbable plant matter like grated avocado pits, minced ginger, garlic, ground pepper, minced turmeric, minced raw yams, minced carrots fresh and sun dried.

All of these minced vegeteables and stems can be sun dried prior to ingestion to reduce absorbability and imitated natural human conditions in the field.
Sun drying of vegetable matter is consistent with human pre-modern feeding practices.

These materials:
occupy intestinal volume
support microbial habitat
prepare fermentation environment
The objective is to fill the digestive tract with cellulose mass.

Phase 3 — Fermentation Activation
Once structural cellulose is present, simple sugars are introduced to activate microbial fermentation.
Examples:
• fruits
• red peppers
• cucumbers
• easily digestible fresh vegetables
• Fermented coldslaw, dills, olives.
• Cheese and milk products

During this phase:
the body remains partially in fasting metabolism
fermentation begins within the cellulose matrix
and microbial populations expands.
This phase nurtures the biome before the host body receives major caloric fat and protein input.

Phase 4 — Transitional Feeding
After several days of fermentation and settling, complex cooked foods are introduced.

Examples:
• lentils
• rice
• legumes
• cooked vegetables
• eggs

These foods nourish both:
the human body
the microbial biome
Cooking at this stage reflects the historical transition that occurred when humans adopted fire.

Phase 5 — Full Feeding Phase
The final stage reintroduces complete dietary freedom.
Foods may include:
• your wife´s cooking
• meats of any type
• complex meals
• traditional or modern foods
• Grandma´s cookies, Pumpkin Pie, Junk food.
• Your mother in law´s famous stew.

At this stage:
• elimination becomes robust and timely
• the digestive system processes dense foods efficiently
• microbial populations remain supported by the cellulose base running its course.
• you still get invited to dinners and parties.

5. Post-Feeding Elimination Window
After the feeding phase:
• elimination may occur over up to three days after stopping the feeding cycle.
During this period:
hunger will increase
the body is clearing accumulated metabolic waste, feels good and wants to binge eat. Let it and you will feel the difference. This will motivate you to start a new cycle.

the intestine empties progressively of cellulose and begins to fill with junk matter, gas and you might begin to retain fluids. Your body begins to act up. You are thinking Pepto Bismol. What you need is to stop and end the cycle by giving your body a chance to reset by resting the stomach.

Waste eliminated includes:
• food residues
• microbial byproducts
• lymphatic wastes
• cellular metabolic byproducts

Any tissue containing living mitochondria generates metabolic waste that must ultimately leave the body as:
• solids
• liquids
• gases

The intestinal tract is the primary route for solid elimination.

6. Cycle Repetition
A new cycle begins when:
• elimination has clearly occurred
• the intestine has run out of useable cellulose and is either partially emptied or filled with food byproducts.
• the body begins to feel the effects of dietary excess

The restart sequence:
short fast
cellulose replenishment
fermentation activation
staged feeding
short fast, getting longer as you "get it".
Real hunger will return after 48 hours or more.

This cyclical process mirrors patterns experienced by humans across long historical periods.

7. Evolutionary Context
For thousands of years, human diets fluctuated between:
• food scarcity
• opportunistic feeding
• high plant bulk consumption

The protocol reflects a structured version of this historical pattern, particularly before cooking became widespread only 15 thousand years ago.

Before cooking was introduced:
humans relied more heavily on plant structural material, sun drying and food storing with out refrigeration.

After cooking was introduced:
complex foods became digestible
staged feeding (three meals a day) likely occurred naturally.

8. Modern Environmental Considerations
Modern food abundance changes the challenge.
Instead of famine or hunting pressure, individuals face:
• constant food availability
• processed foods
• cultural foods (family cooking, comfort foods)
• commercial food chains

Examples:
• homemade meals
• baked goods
• Restaurant food

These foods are not inherently negative. The responsibility lies with the individual to manage intake within a functional digestive cycle.

9. Intended Audience
This protocol is directed toward:
• healthy adults
• individuals without body-weight disorders
• researchers in nutrition inflammation and human physiology
• scientists studying the microbiome

The objective is not calorie restriction or dieting, but rather biological order in:
feeding
microbial support
waste elimination

10. Strategic Outcome
A properly functioning cycle aims to achieve:
• stable intestinal biome
• regular elimination
• reduced systemic inflammation
• orderly cellular metabolism

By allowing each cell to:
receive fuel
perform metabolic work
eliminate waste
the body maintaining physiological equilibrium.

Summary
The protocol organizes eating and fasting into a cyclical model centered on:
intestinal structural filling (cellulose)
controlled microbial fermentation
staged nutritional feeding
robust elimination

This framework prioritizes the intestinal ecosystem as a foundational organ system, recognizing that human metabolic health depends on both the host body and its microbial partners.